Macrocycle Docking Service

Welcome to CD ComputaBio, your premier partner in computational biology solutions. Our macrocycle docking service offers state-of-the-art computational tools and expertise to support your drug discovery and development endeavors. With a focus on innovation and excellence, we provide tailored services to meet your unique research needs. Explore the capabilities of our macrocycle docking service and revolutionize your drug design and optimization strategies.

Applications of Macrocycle Docking

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  Peptide Drug Design

  Explore the feasibility of macrocycles as peptide mimetics for drug design and optimization.
• 

  Cyclotide Screening

  Investigate natural or synthetic cyclic peptides, such as cyclotides, for their potential as drug candidates through macrocycle docking simulations.
• 

  Protein-Protein Interaction Modulation

  Study macrocycles as inhibitors or modulators of protein-protein interactions, facilitating the development of novel therapeutics.

Our Services

• Macrocycle Design
  • Ring Size: The number of atoms in the ring influences the overall properties (flexibility, cavity size, etc.).
  • Conformation: Planar (aromatic macrocycles), twisted, chair-like, etc.
  • Symmetry: Symmetric macrocycles vs. asymmetric structures.
  • Intramolecular Interactions: Hydrogen bonds, π-π interactions, van der Waals forces.

Fig 1. Overall macrocycle design

• Macrocycle Docking
  Efficient sampling of ring conformations is critical to reproducing experimental binding modes in docking experiments, especially for macrocycles where hundreds of low-energy conformations may exist. Glide relies on an extensive database of ring conformations to sample low-energy states that would otherwise not be sampled for macrocyclic ring systems. Generating ring templates for macrocycles can significantly improve native pose predictions.

Fig 2. Macrocycle docking strategy

• Ring Stability Prediction
  Our predictions regarding the ring strain of macrocycles, essential for adopting conformations akin to known active ligands, can be leveraged to screen linkers and identify those that yield high-affinity macrocyclic analogs of linear ligands.

Software and Tools

Our scientists use Glide for molecular docking, integrating macrocycle ring sampling into Glide docking:

• Accurate - 65% of macrocycles self-docked within 2.0 Å RMSD
• Fast - Averages about an hour per compound, including ring sampling and docking

Features of Macrocycle Design Service

• Accurate - Exhibits a median backbone RMSD of 0.40 Å, with minimal outliers exceeding 1.5 Å.
• Diverse - Generates unique output conformations.
• Fast - Achieves median calculation times of 5-10 minutes.
• Scalable - Delivers accurate and diverse results for both cyclic peptides and macrocyclic natural products.

Our Advantags

Confidentiality

Your data security and confidentiality are paramount to us, and we strictly adhere to confidentiality protocols to safeguard your sensitive information.

Collaborative Approach

We cultivate a collaborative partnership with our clients, maintaining open communication and feedback to guarantee the success of every project.

Timely Delivery

We prioritize swift delivery of results without compromising on accuracy or quality, meeting your project timelines effectively.

CD ComputaBio offers comprehensive macrocycle docking services for drug discovery, protein-protein interactions, and structure-based drug design. With our expertise, customized solutions, state-of-the-art technology, and timely delivery, we are your trusted partner for accelerating research in the field of computational biology. If you are interested in our services or have any questions, please feel free to contact us.